LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.6385685 3.6385685 3.6385685 Created orthogonal box = (0.0000000 -65.897278 0.0000000) to (23.298206 65.897278 5.1457129) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2507382 5.6253774 5.1457129 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -65.897278 0.0000000) to (23.298206 65.897278 5.1457129) create_atoms CPU = 0.002 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2507382 5.6253774 5.1457129 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -65.897278 0.0000000) to (23.298206 65.897278 5.1457129) create_atoms CPU = 0.002 seconds 658 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 5 28 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1308 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_097471813275_000#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 5 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 6.340 | 6.340 | 6.340 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3734.4129 0 -3734.4129 108919.4 127 0 -4447.8225 0 -4447.8225 -2402.7591 Loop time of 5.08179 on 1 procs for 127 steps with 1308 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3734.41288219745 -4447.81829974974 -4447.82246230446 Force two-norm initial, final = 1746.8169 0.17405991 Force max component initial, final = 492.58195 0.019399337 Final line search alpha, max atom move = 1.0000000 0.019399337 Iterations, force evaluations = 127 212 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.9401 | 4.9401 | 4.9401 | 0.0 | 97.21 Neigh | 0.096913 | 0.096913 | 0.096913 | 0.0 | 1.91 Comm | 0.026241 | 0.026241 | 0.026241 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01854 | | | 0.36 Nlocal: 1308.00 ave 1308 max 1308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11718.0 ave 11718 max 11718 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 415608.0 ave 415608 max 415608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 415608 Ave neighs/atom = 317.74312 Neighbor list builds = 4 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 5 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 127 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.345 | 6.345 | 6.345 Mbytes Step Temp E_pair E_mol TotEng Press Volume 127 0 -4447.8225 0 -4447.8225 -2402.7591 15800.306 130 0 -4447.8702 0 -4447.8702 1.7680619 15773.787 Loop time of 0.142043 on 1 procs for 3 steps with 1308 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4447.82246230447 -4447.87011644025 -4447.87023789382 Force two-norm initial, final = 51.192291 0.31802990 Force max component initial, final = 40.249129 0.18318559 Final line search alpha, max atom move = 0.00043914458 8.0444959e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13913 | 0.13913 | 0.13913 | 0.0 | 97.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00058906 | 0.00058906 | 0.00058906 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002326 | | | 1.64 Nlocal: 1308.00 ave 1308 max 1308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11718.0 ave 11718 max 11718 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 415632.0 ave 415632 max 415632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 415632 Ave neighs/atom = 317.76147 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 5 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 6.483 | 6.483 | 6.483 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4447.8702 0 -4447.8702 1.7680619 Loop time of 2.185e-06 on 1 procs for 0 steps with 1308 atoms 183.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 2.185e-06 | | |100.00 Nlocal: 1308.00 ave 1308 max 1308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11718.0 ave 11718 max 11718 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 415704.0 ave 415704 max 415704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 415704 Ave neighs/atom = 317.81651 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 5 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 6.483 | 6.483 | 6.483 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -4447.8702 -4447.8702 23.31919 131.65729 5.1378047 1.7680619 1.7680619 5.3442947 -18.587165 18.547056 2.3863389 514.9819 Loop time of 2.462e-06 on 1 procs for 0 steps with 1308 atoms 324.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 2.462e-06 | | |100.00 Nlocal: 1308.00 ave 1308 max 1308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11718.0 ave 11718 max 11718 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 207852.0 ave 207852 max 207852 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 415704.0 ave 415704 max 415704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 415704 Ave neighs/atom = 317.81651 Neighbor list builds = 0 Dangerous builds = 0 1308 -4447.87023789382 eV 2.38633892499255 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05